The Intransitive Logic of Directed Cycles and Flipons Enhances the Evolution of Molecular Computers by Augmenting the Kolmogorov Complexity of Genomes

Dr. Alan Herbert received his medical degree from the University of Auckland in 1979 and completed his PhD in Immunobiology. He worked at MIT in the laboratory of Dr. Alexander Rich (1988–2000). He was an Associate Professor of the Framingham Heart Study at Boston University (2000–2014) and served as a consultant to the Coriell Institute for Medical Research (2007–2013). He worked as an Associate Principal Scientist in Human Genetics and PharmacoGenetics at Merck Research Laboratories (2014–2016). He is currently the founder and head of InsideOutBio (since 2017) and also on the Scientific Advisory Board of Avammune (from 2023 to present). He is best known for his work establishing the existence of Z-DNA- and Z-RNA-binding proteins and for the genetic studies establishing the role of these alternative, left-handed conformations in biology, including the regulation of interferon responses to viruses, cancers and in autoimmunity. His current work focuses on flipons, sequences that form alternative conformations under physiological conditions. Flipons encode genetic information by structure, acting as switches to change genetic programs according to context. Many of the simple repeats that comprise over half of the human genome can act as flipons. They enable rapid evolutionary adaptations by altering the readout of genetic information in soft-wired genomes. The conformation of flipons can be regulated by small RNAs in a sequence-specific manner to further modulate phenotypes.